import(tools, AnnotationDbi)
importFrom(annaffy, "getURL")
importFrom(annaffy, "getHTML")
importFrom(annotate, "organism")
importFrom(rtracklayer, "browserSession", "ucscTableQuery", "tableName", "track")

importClassesFrom("GGBase", "cnumOrMissing")

importClassesFrom(IRanges, RangedData)
importFrom(IRanges, RangedData, space, findOverlaps)

importFrom(graphics,
           abline, axis, boxplot, layout, legend,
           par, 
    plot, 
           points) 

importClassesFrom("GSEABase", "GeneSet")
importFrom("GSEABase", "GeneSet")

importFrom(stats,
           as.formula, formula, lm, resid)

exportClasses( multffManager, maxchisq)

exportMethods(gwSnpTests, plot, topSnps, coerce, 
   show, "[", min_p_vals )
#pvals, locs, hscores, 

#export(snpm2phase, personalHap,
# parsePh.out, snpm2mapLD, masterSnps, chunksize,
# cisSnpTests, aafSNP, slimCisTrans,
## slimCTchr2SQLite, slimCTchr2flat, minp, locreport, 
#  wgtinfo2browser, top4, slimCTchr2ff, ffs2minp, #ffcistrans, 
#  multffCT, makeCommonSNPs, checkCommonSNPs, diagffCC, maxchisq) #, phaseHS)

export( multffCT, makeCommonSNPs, checkCommonSNPs, diagffCC, maxchisq,
   cisSnpTests, geneRanges, snp130locs, bestCis, geneTrack )
# snpm2phase, snpm2mapLD )
